Mutagenetix > Incidental Mutation

Incidental Mutation 'R9026:Rag2'

686709

Institutional Source

Beutler Lab

Gene Symbol

Rag2

Ensembl Gene

ENSMUSG00000032864

Gene Name

recombination activating gene 2

Synonyms

Rag-2

MMRRC Submission

068855-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9026 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

101455063-101462874 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 101460494 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 268 (N268I)

Ref Sequence

ENSEMBL: ENSMUSP00000038204 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044031] [ENSMUST00000099682] [ENSMUST00000111227] [ENSMUST00000111231] [ENSMUST00000128898] [ENSMUST00000160037] [ENSMUST00000160722]

AlphaFold

P21784

PDB Structure

A PHD finger motif in the C-terminus of RAG2 modulates recombination activity [SOLUTION NMR]
Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME1K4ME3 PEPTIDE [X-RAY DIFFRACTION]
Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide [X-RAY DIFFRACTION]
Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide [X-RAY DIFFRACTION]
Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide [X-RAY DIFFRACTION]
Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution [X-RAY DIFFRACTION]
Crystal structure of the core RAG1/2 recombinase [X-RAY DIFFRACTION]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000044031
AA Change: N268I

PolyPhen 2 Score 0.458 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000038204
Gene: ENSMUSG00000032864
AA Change: N268I

Domain	Start	End	E-Value	Type
Pfam:RAG2	51	389	3.5e-179	PFAM
Pfam:RAG2_PHD	414	491	7.2e-50	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000099682

Predicted Effect

possibly damaging
Transcript: ENSMUST00000111227
AA Change: N268I

PolyPhen 2 Score 0.458 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000106858
Gene: ENSMUSG00000032864
AA Change: N268I

Domain	Start	End	E-Value	Type
Pfam:RAG2	51	389	6.7e-193	PFAM
Pfam:RAG2_PHD	414	491	1.1e-50	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000111231

Predicted Effect

probably benign
Transcript: ENSMUST00000128898

Predicted Effect

probably benign
Transcript: ENSMUST00000160037

Predicted Effect

probably benign
Transcript: ENSMUST00000160722

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.2%

Validation Efficiency

100% (81/81)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is involved in the initiation of V(D)J recombination during B and T cell development. This protein forms a complex with the product of the adjacent recombination activating gene 1, and this complex can form double-strand breaks by cleaving DNA at conserved recombination signal sequences. The recombination activating gene 1 component is thought to contain most of the catalytic activity, while the N-terminal of the recombination activating gene 2 component is thought to form a six-bladed propeller in the active core that serves as a binding scaffold for the tight association of the complex with DNA. A C-terminal plant homeodomain finger-like motif in this protein is necessary for interactions with chromatin components, specifically with histone H3 that is trimethylated at lysine 4. Mutations in this gene cause Omenn syndrome, a form of severe combined immunodeficiency associated with autoimmune-like symptoms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit arrested development of T and B cell maturation at the CD4-8- thymocyte or B220+/CD43+pro-B cell stage due to inability to undergo V(D)J recombination. [provided by MGI curators]

Allele List at MGI

All alleles(14) : Targeted(14)

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	C	A	3: 137,770,909 (GRCm39)	Q33K	possibly damaging	Het
Acap2	A	G	16: 30,925,906 (GRCm39)	L550P	probably damaging	Het
Acsm3	A	T	7: 119,373,845 (GRCm39)	S244C	probably benign	Het
Adam28	T	A	14: 68,846,593 (GRCm39)	D740V	probably benign	Het
Adcy4	C	A	14: 56,016,426 (GRCm39)	V342L	probably damaging	Het
Adcyap1r1	A	G	6: 55,458,107 (GRCm39)	T303A	probably benign	Het
Agr2	T	C	12: 36,046,091 (GRCm39)	V74A	probably benign	Het
Akp3	A	T	1: 87,054,786 (GRCm39)	T374S	possibly damaging	Het
Ankrd36	A	T	11: 5,610,696 (GRCm39)	I1181L	probably benign	Het
Arhgap11a	A	T	2: 113,664,411 (GRCm39)	V624E	probably benign	Het
Arhgap30	A	T	1: 171,228,258 (GRCm39)	D112V	probably damaging	Het
Atp8b4	A	G	2: 126,184,883 (GRCm39)	F927L	probably benign	Het
Bend4	C	A	5: 67,584,475 (GRCm39)	G150C	unknown	Het
Cd300lg	T	A	11: 101,944,998 (GRCm39)	S403T	probably damaging	Het
Cep57l1	T	A	10: 41,607,086 (GRCm39)	Q159L	probably damaging	Het
Cipc	C	T	12: 86,999,634 (GRCm39)	T57M	probably damaging	Het
Def8	T	C	8: 124,186,391 (GRCm39)	C377R	probably damaging	Het
Dock1	A	G	7: 134,720,746 (GRCm39)	D1285G	probably damaging	Het
Efcab10	A	G	12: 33,448,398 (GRCm39)	D77G	probably damaging	Het
Eml4	C	T	17: 83,764,479 (GRCm39)	T663M	probably damaging	Het
Ercc8	A	G	13: 108,320,389 (GRCm39)	E325G	possibly damaging	Het
Ermap	C	A	4: 119,035,240 (GRCm39)	A583S	probably damaging	Het
F13a1	C	T	13: 37,102,506 (GRCm39)	G406S	probably null	Het
Faap20	T	A	4: 155,335,426 (GRCm39)	C141S	probably benign	Het
Fam193a	A	G	5: 34,616,536 (GRCm39)	T904A	possibly damaging	Het
Garin2	T	C	12: 78,757,097 (GRCm39)	F18S	probably benign	Het
Gas8	A	G	8: 124,260,134 (GRCm39)	D455G	probably benign	Het
Gm21863	T	C	12: 20,004,521 (GRCm39)	S6P	probably damaging	Het
Gm4841	A	T	18: 60,403,988 (GRCm39)	I35N	probably damaging	Het
Grk4	T	A	5: 34,877,084 (GRCm39)	C260S	probably damaging	Het
Huwe1	G	A	X: 150,716,084 (GRCm39)	R4331Q	unknown	Het
Ighv5-6	A	G	12: 113,589,247 (GRCm39)	Y78H	probably benign	Het
Itpr3	G	A	17: 27,337,651 (GRCm39)		probably benign	Het
Kl	T	A	5: 150,876,491 (GRCm39)	S104T	probably benign	Het
Lyve1	C	A	7: 110,453,182 (GRCm39)	C138F	probably damaging	Het
Med27	G	A	2: 29,399,446 (GRCm39)	W92*	probably null	Het
Mical3	A	T	6: 120,986,848 (GRCm39)		probably benign	Het
Mrgpra4	C	A	7: 47,631,208 (GRCm39)	R131L	possibly damaging	Het
Myf5	T	C	10: 107,321,308 (GRCm39)	N162S	probably benign	Het
Myh15	G	A	16: 49,007,433 (GRCm39)	E1835K	probably damaging	Het
Myo9a	T	A	9: 59,716,757 (GRCm39)	Y486N	probably damaging	Het
Ncapg	T	A	5: 45,853,115 (GRCm39)	N860K	probably benign	Het
Nr4a3	T	C	4: 48,052,194 (GRCm39)	F316S	possibly damaging	Het
Nsd3	T	A	8: 26,172,576 (GRCm39)	S778R	probably benign	Het
Or2r2	A	G	6: 42,463,795 (GRCm39)	F111L	probably damaging	Het
Or4c119	A	T	2: 88,986,988 (GRCm39)	V177E	probably benign	Het
Or4c31	A	G	2: 88,292,196 (GRCm39)	I190V	probably damaging	Het
Or5p6	A	G	7: 107,631,286 (GRCm39)	F88S	probably damaging	Het
Or7e173	T	C	9: 19,938,344 (GRCm39)	N297D		Het
Or8b37	T	A	9: 37,958,885 (GRCm39)	Y122*	probably null	Het
Or8w1	A	T	2: 87,465,369 (GRCm39)	C241S	probably damaging	Het
Or9m2	A	G	2: 87,820,568 (GRCm39)	T38A	probably damaging	Het
Pdlim4	C	T	11: 53,946,280 (GRCm39)	G231S	probably benign	Het
Pknox2	C	T	9: 36,821,044 (GRCm39)	V273I	possibly damaging	Het
Pm20d1	A	G	1: 131,739,822 (GRCm39)	H390R	probably benign	Het
Prkg2	A	T	5: 99,114,386 (GRCm39)	D587E	probably benign	Het
Prps1l1	T	A	12: 35,035,546 (GRCm39)	D220E	possibly damaging	Het
Prss3l	A	G	6: 41,422,990 (GRCm39)	F4L	probably benign	Het
Ptchd3	T	C	11: 121,721,682 (GRCm39)	V185A	possibly damaging	Het
Rarres2	A	G	6: 48,549,020 (GRCm39)		probably null	Het
Rrp12	T	C	19: 41,860,223 (GRCm39)	H1000R	probably benign	Het
S100a2	A	T	3: 90,498,811 (GRCm39)	Y104F	unknown	Het
Sell	A	G	1: 163,893,042 (GRCm39)	Y86C	probably damaging	Het
Serpinb6d	A	T	13: 33,851,656 (GRCm39)	T138S	possibly damaging	Het
Slamf7	T	A	1: 171,466,312 (GRCm39)	I228F	probably benign	Het
Slc11a1	G	A	1: 74,416,325 (GRCm39)	V92M	probably damaging	Het
Spi1	A	G	2: 90,912,862 (GRCm39)	N5S	unknown	Het
Stard9	G	T	2: 120,536,283 (GRCm39)	D4151Y	probably damaging	Het
Stmnd1	A	G	13: 46,452,983 (GRCm39)	T220A	probably benign	Het
Tacc2	G	T	7: 130,225,266 (GRCm39)	W650C	probably damaging	Het
Tmc5	A	G	7: 118,241,594 (GRCm39)	N429S	possibly damaging	Het
Tmem201	A	C	4: 149,812,627 (GRCm39)	L230V	probably benign	Het
Tmem222	T	C	4: 132,997,119 (GRCm39)	E94G	possibly damaging	Het
Trappc4	A	G	9: 44,315,655 (GRCm39)	F186S	probably damaging	Het
Trim17	A	G	11: 58,862,273 (GRCm39)	N435S	probably benign	Het
Trim68	A	T	7: 102,329,447 (GRCm39)	L227Q	probably damaging	Het
Tuba3b	T	G	6: 145,563,996 (GRCm39)	V14G	possibly damaging	Het
Ubr2	G	T	17: 47,245,041 (GRCm39)	H1662N	probably damaging	Het
Vps13c	T	A	9: 67,861,863 (GRCm39)	V2915E	probably damaging	Het
Vsig10	C	T	5: 117,476,323 (GRCm39)	T259I	probably benign	Het
Zfp267	A	G	3: 36,219,066 (GRCm39)	Y363C	possibly damaging	Het

Other mutations in Rag2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00647:Rag2	APN	2	101,460,962 (GRCm39)	missense	probably benign	0.00
IGL01358:Rag2	APN	2	101,460,365 (GRCm39)	missense	possibly damaging	0.95
IGL01774:Rag2	APN	2	101,460,392 (GRCm39)	missense	probably damaging	1.00
IGL02267:Rag2	APN	2	101,460,376 (GRCm39)	missense	probably damaging	1.00
IGL02507:Rag2	APN	2	101,461,055 (GRCm39)	missense	probably damaging	0.99
IGL02615:Rag2	APN	2	101,459,913 (GRCm39)	nonsense	probably null
IGL02690:Rag2	APN	2	101,459,839 (GRCm39)	missense	probably benign	0.00
IGL03087:Rag2	APN	2	101,460,559 (GRCm39)	missense	probably benign	0.00
IGL03261:Rag2	APN	2	101,460,608 (GRCm39)	missense	probably damaging	0.96
billfold	UTSW	2	101,461,118 (GRCm39)	missense	probably damaging	1.00
Brag	UTSW	2	101,460,040 (GRCm39)	missense	probably damaging	1.00
excambiar	UTSW	2	101,461,121 (GRCm39)	missense	probably damaging	0.99
picker	UTSW	2	101,460,419 (GRCm39)	missense	probably damaging	1.00
snowcock	UTSW	2	101,460,948 (GRCm39)	missense	probably damaging	1.00
woodcock	UTSW	2	101,460,464 (GRCm39)	missense	probably damaging	0.98
R0266:Rag2	UTSW	2	101,460,948 (GRCm39)	missense	probably damaging	1.00
R0284:Rag2	UTSW	2	101,460,464 (GRCm39)	missense	probably damaging	0.98
R1250:Rag2	UTSW	2	101,460,784 (GRCm39)	missense	probably damaging	0.96
R1520:Rag2	UTSW	2	101,460,476 (GRCm39)	missense	probably damaging	0.99
R1641:Rag2	UTSW	2	101,459,960 (GRCm39)	missense	probably benign	0.22
R2260:Rag2	UTSW	2	101,460,583 (GRCm39)	missense	probably benign	0.00
R2571:Rag2	UTSW	2	101,460,312 (GRCm39)	missense	probably damaging	0.99
R3441:Rag2	UTSW	2	101,460,645 (GRCm39)	missense	probably damaging	0.99
R3752:Rag2	UTSW	2	101,461,121 (GRCm39)	missense	probably damaging	0.99
R4894:Rag2	UTSW	2	101,460,022 (GRCm39)	missense	probably damaging	1.00
R5197:Rag2	UTSW	2	101,461,085 (GRCm39)	missense	probably damaging	1.00
R5236:Rag2	UTSW	2	101,460,005 (GRCm39)	missense	probably damaging	1.00
R6815:Rag2	UTSW	2	101,460,900 (GRCm39)	missense	probably damaging	0.99
R7365:Rag2	UTSW	2	101,461,118 (GRCm39)	missense	probably damaging	1.00
R7917:Rag2	UTSW	2	101,460,040 (GRCm39)	missense	probably damaging	1.00
R9243:Rag2	UTSW	2	101,460,419 (GRCm39)	missense	probably damaging	1.00
R9280:Rag2	UTSW	2	101,460,145 (GRCm39)	missense	probably benign	0.05
R9333:Rag2	UTSW	2	101,460,752 (GRCm39)	missense	probably benign	0.01
R9500:Rag2	UTSW	2	101,461,217 (GRCm39)	missense	probably damaging	1.00
X0027:Rag2	UTSW	2	101,460,718 (GRCm39)	missense	probably damaging	1.00
Z31818:Rag2	UTSW	2	101,461,150 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGAACTTCAGGATGGGCTGTC -3'
(R):5'- TATGCCAAGGAAAATAGTCCCG -3'

Sequencing Primer
(F):5'- AACTTCAGGATGGGCTGTCTTTTC -3'
(R):5'- GGAAAATAGTCCCGTTTCCCATG -3'

Posted On

2021-11-19